Re: [Freesurfer] errors on the WM and Gray inflated surfaces

] errors on the WM and Gray inflated surfaces Hi Pablo if it has the extension .label then it is a label not an annotation, and you should load it as such cheers Bruce On Fri, 8 Apr 2016, pablo najt wrote: > Thank you Bruce for the response.Actually the surface works in freeview just >

Re: [Freesurfer] errors on the WM and Gray inflated surfaces

ook ok with freeview? It might just be a display problem On Apr 8, 2016, at 9:26 AM, pablo najt <pablon...@hotmail.com> wrote: Dear FS expert and users,We are coming across errors on the WM and Gray inflated surfaces.When trying to open the surfaces with tksurfer as follows (tksurfer subid lh i

Re: [Freesurfer] errors on the WM and Gray inflated surfaces

Dear FS expert and users,We are coming across errors on the WM and Gray inflated surfaces.When trying to open the surfaces with tksurfer as follows (tksurfer subid lh inflated -gray) We get only a small part of the cortex displaying. Also when we try

Re: [Freesurfer] Difficulty correcting Pial surfaces

Dear experts and FS users,I came across the following problem it would be useful help if anyone is able to advice.ThanksPablo I am having issues when trying to remove non cortical tissue (mostly skull). I load my images as follow: freeview -v mri/T1.mgz mri/brainmask.mgz -f

[Freesurfer] Difficulty correcting Pial surfaces

Dear FS experts.I am having issues when trying to remove non cortical tissue (mostly skull). I load my images as follow: freeview -v mri/T1.mgz mri/brainmask.mgz -f surf/lh.white:edgecolor=yellow surf/lh.pial:edgecolor=red surf/rh.white:edgecolor=yellow surf/rh.pial:edgecolor=r Then I

Re: [Freesurfer] A mixed effect model approach in within subject dataset {Disarmed}

the sort command). Best, Martin On 10/27/2015 01:32 PM, pablo najt wrote: Thank you for your input. I noticed that if I follow literally all the steps in the wiki, my data which is ordered by variable 'family

Re: [Freesurfer] A mixed effect model approach in within subject dataset {Disarmed} {Disarmed}

you are doing. Best, Martin On 11/03/2015 12:01 PM, pablo najt wrote: Dear Martin and FS experts. I have a quick query about how to obtain my design matrix of group by age from the following matlab command listed

Re: [Freesurfer] A mixed effect model approach in within subject dataset {Disarmed}

this to get the ni: [M,Y,ni] = sortData(M,1,Y,sID); # (sorts the data) see https://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels hope that helps, Martin On 10/14/2015 10:43 AM, pablo najt wrote: Dear FS experts

[Freesurfer] Display pctdiff only cluster surviving multiple comparisons

Thank you, Doug.I have computed the percent difference between a 2-group comparison. However when I open the results the percent difference is showing all over the cortex. Instead I would like to only display the percent difference in the area that survived multiple comparisons. Is there a way

[Freesurfer] Contrast for a group diff correlation with age

Hello FS experts,I have a question about setting the following contrast in mri_glmfitMy contrast of interest:Does area.pial --age correlation, accounting for gender, differ between PT and HC? Class Female_PTClass Female_HCClass Male_PTClass Male_HCIf I set my classes are as above, should my

Re: [Freesurfer] A mixed effect model approach in within subject dataset {Disarmed}

with the ordering of the design matrix and its correspondence with the ordering of the ni vector or the ordering of the image data etc... You will need to check it thoroughly. Cheers-Jorge De: pablo najt <pablon...@hotmail.com> Para: "freesurfer@nmr.mgh.harvard.edu&q

Re: [Freesurfer] Volumes differ in acquisition paramaters

Dear Martin and FS experts.I am having difficulty in loading my qdec.table.dat to Matlab.When I use the [command: Qdec = fReadQdec('qdec.table.dat'); ] Matlab only recognises a matrix of 140x1 cell, whereas instead it should recognise a 140x4.I tried to import the table as 'table' from the gui

Re: [Freesurfer] A mixed effect model approach in within subject dataset {Disarmed}

like this to get the ni: [M,Y,ni] = sortData(M,1,Y,sID); # (sorts the data) see https://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels hope that helps, Martin On 10/14/2015 10:43 AM, pablo najt wrote:

Re: [Freesurfer] A mixed effect model approach in within subject dataset {Disarmed}

ni, lhcortex, [], 4); Please make sure that sum(ni) and length(X) give the same value before running the above command. Cheers-Jorge De: pablo najt <pablon...@hotmail.com> Para: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Enviado: Jueves 15 de octubre de 2015 7

Re: [Freesurfer] A mixed effect model approach in within subject dataset {Disarmed}

ntercept term and age as random effects. Hope that helps Cheers -Jorge De: pablo najt <pablon...@hotmail.com> Para: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> Enviado: Jueves 10 de septiembre de 2015 8:07 Asunto: [Frees

Re: [Freesurfer] repeated measures ANOVA using the FSGD file

Hello FS experts,I am reposting as a good few emails went by after me posting. My question is below.Thank you for your help.Pablo From: pablon...@hotmail.com To: freesurfer@nmr.mgh.harvard.edu Date: Tue, 6 Oct 2015 13:53:21 + Subject: [Freesurfer] repeated measures ANOVA using the FSGD file

[Freesurfer] repeated measures ANOVA using the FSGD file

Dear FS expertsTrying to set up a Linear Mixed Effects, which I understand would basically be a repeated measures design. My design has 3 groups (HC, PT relatives and PT).Instead of time points of the same subject my design matrix uses each family member within a family. So I will have many

[Freesurfer] FSGD for A mixed effect model approach in within subject dataset

but considering both the intercept term and age as random effects. Hope that helps Cheers -Jorge De: pablo najt <pablon...@hotmail.com> Para: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> Enviado: Jueves 10 de septiembre de 2015 8:07 Asunto

[Freesurfer] Test incoming emails -

I am sending this message as a test since my income emails from FS stopped working on the 29 of September.Regards ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] Question about the multiple comparison correction in FreeSurfer {Disarmed}

Thank you! Date: Mon, 21 Sep 2015 23:43:39 -0400 From: gr...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Question about the multiple comparison correction in FreeSurfer On 9/21/15 9:15 PM, chenhf_uestc wrote:

Re: [Freesurfer] Qdec: group differences covaring for age and sex {Disarmed}

looks like you are using Sex as a continuous covariate? That > is not correct. It should be discrete. So you should have 4 classes > (HC-M, HC-F, PT-M, PT-F) > > On 09/21/2015 09:31 AM, pablo najt wrote: > > Hello FS experts, > > I would like to understand the results

[Freesurfer] Qdec: group differences covaring for age and sex

Hello FS experts,I would like to understand the results from qdec in a GLM model with Group (PT/HC), and two covariates (Age, gender).I set up my contrast as follow: Group DiffHC PT AgeHC AgePT SexHC SexPT 1 -10 0 0 0 Group x Age effectHC PT AgeHC

Re: [Freesurfer] Magnitude of group difference

ks! > To: freesurfer@nmr.mgh.harvard.edu > From: gr...@nmr.mgh.harvard.edu > Date: Fri, 18 Sep 2015 15:00:40 -0400 > Subject: Re: [Freesurfer] Magnitude of group difference > > > > On 09/18/2015 02:37 PM, pablo najt wrote: > > Hello Doug, > > Below you suggested

Re: [Freesurfer] Magnitude of group difference

can compute the percent differences from the average in the cluster. For this you'll need to load the y file for the clusters and sort the subjects (rows) into groups and compute the precentage difference. On 8/28/15 4:54 AM, pablo najt wrote

Re: [Freesurfer] Error downloading fs dataset

Curl couldn't write data to a local filesystem or similar." Best, Lee On Fri, 18 Sep 2015, pablo najt wrote: > Dear FS experts and users, > I am coming across an error -see below, when trying to download buckner > dataset from the terminal. Any tips as to how to overcome this

[Freesurfer] Error downloading fs dataset

Dear FS experts and users, I am coming across an error -see below, when trying to download buckner dataset from the terminal. Any tips as to how to overcome this would be greatly appreciated. Thanks! Pablo [localhost:/Volumes/NEW_VOLUME/FS_dataset] % curl -O

[Freesurfer] Resolved - RE: Error downloading fs dataset

error. Curl couldn't write data to a local filesystem or similar." Best, Lee On Fri, 18 Sep 2015, pablo najt wrote: > Dear FS experts and users, > I am coming across an error -see below, when trying to download buckner > dataset from the terminal. Any tips as to how to

[Freesurfer] FW: problem installing Bernal's Linear Mixed Effects (LME) Models

t can only be the intercept term or any covariate that varies within family. For example you can compare a model with a single random effect for the intercept term against the same model but considering both the intercept term and age as random effects. Hope that helps Cheers -Jorge De:

[Freesurfer] A mixed effect model approach: Qdec possible with three group study design?

the intercept term and age as random effects. Hope that helps Cheers -Jorge De: pablo najt <pablon...@hotmail.com> Para: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> Enviado: Jueves 10 de septiembre de 2015 8:07 Asunto: [Free

[Freesurfer] A mixed effect model approach in within subject dataset

Dear Freesurfer users,I wanted to enquire if anyone had successfully been able to implement Bernal's Linear Mixed Effects (LME) Models in cross-section dataset *not longitudinal* (please see previous thread below). I am willing to perform a LME (3 groups (HC, PT and Unaffected_relatives)

Re: [Freesurfer] A mixed effect model approach in within subject dataset

as random effects. Hope that helps Cheers -Jorge De: pablo najt <pablon...@hotmail.com> Para: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> Enviado: Jueves 10 de septiembre de 2015 8:07 Asunto: [Freesurfer] A mixed effect model appr

Re: [Freesurfer] problem installing Bernal's Linear Mixed Effects (LME) Models

as random effects. Hope that helps Cheers -Jorge De: pablo najt <pablon...@hotmail.com> Para: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> Enviado: Jueves 10 de septiembre de 2015 8:07 Asunto: [Freesurfer] A mixed effect model ap

[Freesurfer] Magnitude of group difference

Hello FS experts and all,I would like to find out the magnitude of the group difference between a two-group comparison (e.g. percent difference on cortical thickness indicating how much one group differs from the other.) I have run analysis using both mri_glmfit and qdec, I also run cluster

[Freesurfer] extract values of individual cluster‏

Dear FS experts,Reposting my message below.Thanks I have run two group comparison on qdec and I get differences in a number of clusters, which also survive cluster wise correction. I would like to extract the values for each of my subjects (to run further stats) on each of these clusters. Is

[Freesurfer] extract values of individual cluster

Dear FS experts, I have run two group comparison on qdec and I get differences in a number of clusters, which also survive cluster wise correction. I would like to extract the values for each of my subjects (to run further stats) on each of these clusters. Is there a way to do this rather than

Re: [Freesurfer] FW: Permutation output

? The log file that has perm in the name? On 8/12/15 11:33 AM, pablo najt wrote: Will do that from now on. the output is as follow: This is the output I am getting which I believe is not what I need for check the permutation output

Re: [Freesurfer] FW: Permutation output

us a tiff On 08/12/2015 11:12 AM, pablo najt wrote: Dear FS exp, In case my message got swamped, I am reposting my question. Many thanks! Pablo From: pablon...@hotmail.com To: freesurfer@nmr.mgh.harvard.edu

[Freesurfer] Permutation output

those other two options. To do this, you'll need to run mri_glmfit-sim from the command line using the --sim perm option. Run it with --help to get examples On 8/7/15 6:59 AM, pablo najt wrote: Dear FS experts, I have a question about running

[Freesurfer] qdec - Generate stats data table

Dear FS experts,I am trying to generate my stats data tables with QDEC -after successfully loading my data table- and come across the following error.Any recommendations would be greatly appreciated.Thank you in advancePabloData table loading completed successfully. SUBJECTS_DIR is

Re: [Freesurfer] qdec - Generate stats data table

12:04 PM, pablo najt wrote: Thank you this subject had a zip copy of the wmparc.stats Now I am missing this file from another subject. Do I need to run recon-all from start or is there a shortcut for getting this file? Thanks Doug. Pablo Date: Tue, 4 Aug 2015 11:42:43 -0400 From

Re: [Freesurfer] qdec - Generate stats data table

@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] qdec - Generate stats data table Have you looked in /Volumes/NEW_VOLUME/GBS/117AS/stats/wmparc.stats to see if there might be a problem? On 08/04/2015 05:43 AM, pablo najt wrote: Dear FS experts, I am trying to generate my stats data tables

Re: [Freesurfer] 3 Group comparison

--surface fsaverage hemi where hemi is lh or rh doug On 07/07/2015 06:45 AM, pablo najt wrote: Dear FS experts, I am trying to run a 3 group comparison with FS. I have run preproc ( script from ENIGMA Cortical protocol) on my first fsgd file. As I have three groups I have prepared

[Freesurfer] 3 group comparison

Dear FS experts following to my query below I run into further errors. If anyone could advice it would be great help.Regards,Pablomri_glmfit \ --y lh.g3v0.thickness.10B.mgh \ --fsgd g3v0.fsgd dods\ --C HC-BD_fam.mtx \ --surf fsaverage lh \ --cortex \ --glmdir lh.g3v0.glmdir? --y

[Freesurfer] 3 Group comparison

Dear FS experts,I am trying to run a 3 group comparison with FS.I have run preproc ( script from ENIGMA Cortical protocol) on my first fsgd file. As I have three groups I have prepared my second fsgd file as g3v0.fsgd and all my desired contrasts, rather than using QDEC. I run this second stage

Re: [Freesurfer] FW: Error #@# MotionCor {Disarmed}

fsaverage which is not what you want. cheers Bruce On Sat, 9 May 2015, pablo najt wrote: Hello I guess my message got lost in the long mailing list. If anyone is able to advice on the message I will be grateful to you. Thanks Pablo

[Freesurfer] Batch processing

Dear FS experts, I am trying to run recon-all -i plus recon-all -all in a for loop to run trough 250 subjects as efficient as possible. I am using OSX any suggestions from previous cases? Thank you for your help, Pablo

Re: [Freesurfer] Analyze format

? cheers Bruce On Wed, 25 Feb 2015, pablo najt wrote: Dear FS experts,I am trying to run recon-all on data with analyze format. I am aware that this is not the best format, however I do not have DICOM or NIFTI original data as this is a very old data from University of North Carolina. When I

[Freesurfer] Analyze format

Dear FS experts,I am trying to run recon-all on data with analyze format. I am aware that this is not the best format, however I do not have DICOM or NIFTI original data as this is a very old data from University of North Carolina. When I run import the images with recon-all -i. I am getting the

[Freesurfer] Strange background when opening brain mask

FreeSurfer experts,I have a question about one of my scans after running recon-all -all. When I open the image with freeview for inspecting brain mask volume.To give you a better idea of the problem I have attached a screenshot of the T1 volume. All my other images did not show the coloured

Re: [Freesurfer] Output of recon-all -all -openmp 8 does not show brainmask.mgz

directory. Sorry for the confusion. -Zeke On 12/13/2013 04:48 PM, pablo najt wrote: Dear Zeke, Thank you so much. As I am not sure which is the log file that we use I am attaching mri_nu (in mri directory) and talairach_avi (in mri/transformations directory). Thanks, Pablo

[Freesurfer] Output of recon-all -all -openmp 8 does not show brainmask.mgz

Dear FS, I am checking on the outputs of recon-all -all using the flag -openmp 8. As I did with standard recon-all -all comand line I was trying to check brainmask.mgz, but there is not such file. Is there anything wrong with my outputs? Or I should be checking a different file? Thank you,

[Freesurfer] FW: -openmp 8 flag for recon-all

, probably at least 32G) cheers Bruce On Tue, 26 Nov 2013, pablo najt wrote: Dear Bruce,Last week I emailed with the question of how many recon -all separate subjects I could run in parallel with the FS version 5.3 for Cent os 6. You answered that this depends on how many

[Freesurfer] -openmp 8 flag for recon-all

, pablo najt wrote: Dear Bruce,Last week I emailed with the question of how many recon -all separate subjects I could run in parallel with the FS version 5.3 for Cent os 6. You answered that this depends on how many cores my machine has. I just found out that our workstation has

[Freesurfer] FW: recon -all in FS version 5.3 CentOS 6

PM, pablo najt pablon...@hotmail.com mailto:pablon...@hotmail.com wrote: Dear FS experts, I am forwarding my question (please see below), in case it got lost among the intense flow of messages. Thank you for your consideration. Pablo

Re: [Freesurfer] recon -all in FS version 5.3 CentOS 6

: [Freesurfer] recon -all in FS version 5.3 CentOS 6 Hi Pablo it depends on how many cores you have Bruce On Thu, 21 Nov 2013, pablo najt wrote: Dear FS experts,I have one question about FS version 5.3 for CentOS 6. I am wondering up to how many recon -all for separate subjects I can run in parallel

Re: [Freesurfer] recon -all in FS version 5.3 CentOS 6

depends on how much ram it has. You should be able to run 1 significantly faster using the -openmp 8 flag to recon-all, or 8 (if you have enough ram, probably at least 32G) cheers Bruce On Tue, 26 Nov 2013, pablo najt wrote: Dear Bruce,Last week I emailed with the question of how many recon -all

Re: [Freesurfer] recon -all in FS version 5.3 CentOS 6

/journal.pone.0038234). for the CentOS 6 you should install CentOS 6 (if you want version 4 it works too). regards! Gari On Wed, Nov 20, 2013 at 5:58 PM, pablo najt pablon...@hotmail.com mailto:pablon...@hotmail.com wrote: Dear FS experts

[Freesurfer] recon -all in FS version 5.3 CentOS 6

CentOS 6, if you have some other requirements maybe Nick or Zeke could help you better, I am just an user :) On Wed, Nov 20, 2013 at 6:47 PM, pablo najt pablon...@hotmail.com mailto:pablon...@hotmail.com wrote: Dear Gari, Thank you for the advice. One additional question

Re: [Freesurfer] Compatibility between RELEASE_I386 i386 and CentOS 6

Dear FS experts,I am forwarding my question (please see below), in case it got lost among the intense flow of messages.Thank you for your consideration.Pablo From: pablon...@hotmail.com To: freesurfer@nmr.mgh.harvard.edu Date: Mon, 18 Nov 2013 16:38:41 + Subject: [Freesurfer] Compatibility

Re: [Freesurfer] Compatibility between RELEASE_I386 i386 and CentOS 6

version 4 it works too).regards!Gari On Wed, Nov 20, 2013 at 5:58 PM, pablo najt pablon...@hotmail.com wrote: Dear FS experts,I am forwarding my question (please see below), in case it got lost among the intense flow of messages.Thank you for your consideration.Pablo From: pablon

Re: [Freesurfer] Compatibility between RELEASE_I386 i386 and CentOS 6

you better, I am just an user :) On Wed, Nov 20, 2013 at 6:47 PM, pablo najt pablon...@hotmail.com mailto:pablon...@hotmail.com wrote: Dear Gari, Thank you for the advice. One additional question. Considering that I will start from scratch the processing

[Freesurfer] Compatibility between RELEASE_I386 i386 and CentOS 6

Dear FS experts,I have a question about compatibility for running recon-all (longitudinal stream) between CentOS 6 x86_64 (64bit) and Mac SnowLeopard OS X 10.6 (32b Intel). I already run recon all- for several of my subjects with a Mac Book Pro with Snow Leopard (using Release_I386 i386).

Re: [Freesurfer] Talairach Failure Detection

On Tue, 27 Aug 2013, pablo najt wrote: Thank you very much for your input. Yes, I did start with analyze format and also I have visually inspected the images. Almost all my scans consistently show an extended whole in the prefrontal area (with a few exception of some scans showing

Re: [Freesurfer] Talairach Failure Detection

, 30 Aug 2013, pablo najt wrote: Dear FS, Following on my question about the initial format of my files for running recon -all, I finally managed to get the Dicom files for our images. However, as the imaging protocol includes several modalities, (resting state, functional, T1, DTI), we had

[Freesurfer] Talairach Failure Detection

Dear FS experts,I am contacting you to report an error after launching recon -all for one of my subjects (see below). I am using a macbook pro with snow leopard version 10.6.8. I would greatly appreciate if you could advise me which step/s should I take to correct this.Thank you for your

Re: [Freesurfer] Talairach Failure Detection

, pablo najt wrote: Dear FS experts,I am contacting you to report an error after launching recon -all for one of my subjects (see below). I am using a macbook pro with snow leopard version 10.6.8. I would greatly appreciate if you could advise me which step/s should I take to correct

Re: [Freesurfer] Talairach Failure Detection

are best On Tue, 27 Aug 2013, pablo najt wrote: Thank you very much for your input. Yes, I did start with analyze format and also I have visually inspected the images. Almost all my scans consistently show an extended whole in the prefrontal area (with a few exception of some scans showing

[Freesurfer] Talairach Failure Detection

Dear FS experts,I am contacting you to report an error after launching recon -all for one of my subjects. I am using a macbook pro with snow leopard version 10.6.8. I would greatly appreciate if you could advise me which step/s should I take to correct this.Thank you for your

[Freesurfer] Freesurfer installation

Dear Freesurfer experts, I have a question regarding the installation/running of FreeSurfer. I have been trying to install freesurfer in a macbook pro (snow leopard) but no success. I followed the webpage from freesurfer (link below).

[Freesurfer] Cortical surface

Dear Freesurfer experts, I am interested in running cortical surface area on longitudinal data from MRI scans and run multisubject comparisons (patients vs controls). I would like to ask you where could I find either a tutorial or a guide for performing

[Freesurfer] Environment variable HOME_FREESURFER

Dear Freesurfer experts, I am trying to install free surfer. It seems that my downloaded version does not have a .cshrc file. I only have an .sh and .csh file. All the edits (i.e.,setenv FREESURFER_HOME Applications/freesurfer/ source Applications/freesurfer/SetUpFreeSurfer.csh) that I

[Freesurfer] environment variable FREESURFER_HOME

Can anyone advice me on how to set the environment variable FREESURFER_HOME for installing it in OS X 10.6.8 (with XQuartz installed)? My directory for Freesurfer: /Applications/freesurfer I know I also have to add: setenv FREESURFER_HOME /Applications/freesurfer source

[Freesurfer] Enquire about running FreeSurfer {Disarmed}

Hello I have a question regarding the installation/running FreeSurfer.I have just completed the installation and got the confirmation that Free surfer was installed. Please see snapshot.However when I follow the steps for testing (https://surfer.nmr.mgh.harvard.edu/fswiki/TestingFreeSurfer), I

Re: [Freesurfer] Enquire about running FreeSurfer {Disarmed}

@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Enquire about running FreeSurfer {Disarmed} Hi Pablo, please respond to the list and not to us directly. Please just cut and paste the text of the error into the email. thanks doug On 06/06/2013 12:30 PM, pablo najt wrote: Thank you for your quick

Re: [Freesurfer] Enquire about running FreeSurfer {Disarmed}

to put the FreeSurfer environment variables into your .cshrc file to have it be in effect every time you open a new shell. doug On 06/06/2013 02:14 PM, pablo najt wrote: Hello My previous problem seemed to be fixed by reinstalling xquartz. However, the strange thing that I get